Guides
- What is NEURON
- A flexible and powerful simulator of neurons and networks
- Advantages over general-purpose simulators
- Separates biology from purely computational concerns
- Convenient user interface
- User-extendable library of biophysical mechanisms
- Enhancements for modeling networks
- Customizable initialization and simulation flow control
- Large user base
- Development, support, and documentation
- Availability and system requirements
- References
- How to get started with NEURON
- Biology Modeling FAQ
- How do I work with neuron morphologies?
- How do I simulate a current clamp pulse experiment?
- How do I simulate a current clamp with non-pulse behavior?
- How do I make cytosolic concentrations change in response to ion channel activity?
- How do I make cytosolic concentrations diffuse and respond to ion channel activity?
- Units used in NEURON
- Using Session Files for Saving and Retrieving Windows
- Using the Cell Builder GUI
- Using the Import3D GUI
- Network Builder tutorials
- Using NEURON’s Optimization Tools
- Randomness in NEURON models
- Frequently asked questions (FAQ)
- Now that I’ve installed NEURON, how do I run it?
- What’s the best way to learn how to use NEURON?
- How do I create a NEURON model?
- Help! I’m having a hard time implementing models!
- Why can’t NEURON read the text file (or
hoc
file) that I created? - How do I print a hard copy of a NEURON window?
- How do I plot something other than membrane potential?
- How do I save and edit figures?
- I’ve used the NEURON Main Menu to construct and manage models. How can I save what I have done?
- What is a ses (session) file? Can I edit it?
- How do I use NEURON’s tools for electrotonic analysis?
- Why should I use an odd value for nseg?
- What’s a good stretegy for specifying nseg?
- How do I change the background color used in NEURON’s shape plots and other graphs?
- How do I change the color scale used in shape plots?
- I see an error message that says … procedure too big in ./foo.hoc …
- Where can I find examples of mod files?
- How do I compile mod files?
- I can’t get mod files to compile.
- I installed a new version of NEURON, and now I see error messages like this: ‘mecanisms fooba needs to be re-translated. its version 5.2 “c” code is incompatible with this neuron version’.
- Is there a list of functions that are built into NMODL?
- Is there a list of functions that are built into hoc?
- What units does NEURON use for current, concentration, etc.?
- When I type a new value into a numeric field, it doesn’t seem to have any effect.
- What is the difference between SEClamp and VClamp, and which should I use?
- SEClamp and IClamp just deliver rectangular step waveforms. How can I make them produce an arbitrary waveform, e.g. something that I calculated or recorded from a real cell?
- I just want a current clamp that will deliver a sequence of current pulses at regular intervals. Vector play seems like overkill for this.
- I want a current clamp that will generate a pulse when I send it an event, or that I can use to produce pulses at precalculated times.
- I have a set of recorded or calculated spike times. How can I use these to drive a postsynaptic mechanism?
- How can I read data from a binary PClamp file?
- How do I exit NEURON? I’m not using the GUI, and when I enter ^D at the oc> prompt it doesn’t do anything?
- Is there a list of functions that are built into NEURON?